@article{fdi:010062023,
  title = {{T}ranscriptome population genomics reveals severe bottleneck and domestication cost in the {A}frican rice ({O}ryza glaberrima)},
  author = {{N}abholz, {B}. and {S}arah, {G}. and {S}abot, {F}ran{\c{c}}ois and {R}uiz, {M}. and {A}dam, {H}{\'e}l{\`e}ne and {N}idelet, {S}. and {G}hesqui{\`e}re, {A}lain and {S}antoni, {S}. and {D}avid, {J}. and {G}lemin, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he {A}frican cultivated rice ({O}ryza glaberrima) was domesticated in {W}est {A}frica 3000years ago. {A}lthough less cultivated than the {A}sian rice ({O}.sativa), {O}.glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). {H}ere, using {RNA}-seq technology, we were able to compare more than 12000 transcripts between 9 {O}.glaberrima, 10 wild {O}.barthii and one {O}.meridionalis individuals. {W}ith a synonymous nucleotide diversity (s)=0.0006 per site, {O}.glaberrima appears as the least genetically diverse crop grass ever documented. {U}sing approximate {B}ayesian computation, we estimated that {O}.glaberrima experienced a severe bottleneck during domestication. {T}his demographic scenario almost fully accounts for the pattern of genetic diversity across {O}.glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. {M}oreover, the large excess of derived nonsynonymous substitution that we detected suggests that the {O}.glaberrima population suffered from the cost of domestication'. {I}n addition, we used this genome-scale data set to demonstrate that (i) {O}.barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6{M}b) exhibits a clear signature of introgression with a yet unidentified {O}ryza species. {T}his work represents the first genome-wide survey of the {A}frican rice genetic diversity and paves the way for further comparison between the {A}frican and the {A}sian rice, notably regarding the genetics underlying domestication traits.},
  keywords = {bottleneck ; cost of domestication ; domestication ; nucleotide diversity ; {O}ryza glaberrima ; {RNA}-seq},
  booktitle = {},
  journal = {{M}olecular {E}cology},
  volume = {23},
  numero = {9},
  pages = {2210--2227},
  ISSN = {0962-1083},
  year = {2014},
  DOI = {10.1111/mec.12738},
  URL = {https://www.documentation.ird.fr/hor/fdi:010062023},
}